Chlorine in PDB 5zdr: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 5zdr was solved by T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.81 / 2.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.308, 219.682, 63.481, 90.00, 114.89, 90.00
R / Rfree (%)	20.7 / 25.7

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Chlorine atom in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative (pdb code 5zdr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 5zdr:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:34.7 occ:1.00 CLAW A:CHW504 0.0 34.7 1.0 CAV A:CHW504 1.8 28.7 1.0 CAP A:CHW504 2.7 25.9 1.0 CAU A:CHW504 2.7 28.8 1.0 OAQ A:CHW504 2.9 23.8 1.0 CAX A:CHW504 3.0 31.5 1.0 CG2 A:THR219 3.9 27.8 1.0 CAC A:CHW504 4.0 27.3 1.0 CD1 A:LEU122 4.0 26.5 1.0 CB A:THR219 4.1 27.7 1.0 CAO A:CHW504 4.1 30.2 1.0 NE A:ARG118 4.1 27.5 1.0 CZ A:TYR220 4.2 36.1 1.0 SG A:CYS119 4.3 50.3 1.0 OH A:TYR220 4.4 36.1 1.0 CA A:CYS119 4.4 37.8 1.0 OG1 A:THR219 4.4 26.8 1.0 CE2 A:TYR220 4.4 36.3 1.0 CAB A:CHW504 4.5 29.0 1.0 CG A:ARG118 4.5 30.1 1.0 CE1 A:TYR220 4.6 35.8 1.0 CD A:ARG118 4.6 27.3 1.0 CB A:CYS119 4.6 40.3 1.0 N A:CYS119 4.7 36.9 1.0 CB A:LEU122 4.9 27.5 1.0 CD2 A:TYR220 5.0 37.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:44.0 occ:1.00 CLAW B:CHW504 0.0 44.0 1.0 CAV B:CHW504 1.8 39.6 1.0 CAP B:CHW504 2.7 42.9 1.0 CAU B:CHW504 2.7 40.1 1.0 OAQ B:CHW504 2.8 40.5 1.0 CAX B:CHW504 2.9 39.0 1.0 SG B:CYS119 3.6 44.0 1.0 CG2 B:THR219 3.7 31.8 1.0 CD1 B:LEU122 3.8 29.0 1.0 CAC B:CHW504 4.0 44.0 1.0 CAO B:CHW504 4.1 38.0 1.0 CB B:THR219 4.1 29.4 1.0 NE B:ARG118 4.1 31.1 1.0 CD B:ARG118 4.3 32.7 1.0 CA B:CYS119 4.3 38.0 1.0 CG B:ARG118 4.4 35.3 1.0 CZ B:TYR220 4.4 29.2 1.0 OG1 B:THR219 4.4 31.3 1.0 OH B:TYR220 4.4 26.1 1.0 CB B:CYS119 4.4 39.1 1.0 CB B:LEU122 4.5 29.9 1.0 CAB B:CHW504 4.5 41.3 1.0 CE2 B:TYR220 4.6 27.4 1.0 CG B:LEU122 4.7 31.4 1.0 CE1 B:TYR220 4.8 31.1 1.0 N B:CYS119 4.8 39.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl504 b:54.9 occ:1.00 CLAW C:CHW504 0.0 54.9 1.0 CAV C:CHW504 1.8 51.7 1.0 CAU C:CHW504 2.7 56.9 1.0 CAP C:CHW504 2.7 48.4 1.0 OAQ C:CHW504 2.9 44.7 1.0 CAX C:CHW504 2.9 57.0 1.0 CG2 C:THR219 3.3 39.9 1.0 CB C:THR219 3.6 41.3 1.0 CD1 C:LEU122 3.6 45.8 1.0 OG1 C:THR219 3.6 42.5 1.0 NE C:ARG118 3.8 50.8 1.0 CAC C:CHW504 4.0 49.2 1.0 CAO C:CHW504 4.1 56.1 1.0 CD C:ARG118 4.4 49.3 1.0 SG C:CYS119 4.5 57.2 1.0 CA C:CYS119 4.5 47.0 1.0 CB C:LEU122 4.5 47.5 1.0 CAB C:CHW504 4.6 52.0 1.0 CG C:ARG118 4.6 47.6 1.0 CZ C:TYR220 4.6 41.8 1.0 CG C:LEU122 4.6 48.7 1.0 OH C:TYR220 4.6 44.7 1.0 CZ C:ARG118 4.6 51.1 1.0 NH2 C:ARG118 4.7 49.9 1.0 CE2 C:TYR220 4.9 41.0 1.0 CB C:CYS119 4.9 49.6 1.0 CE1 C:TYR220 5.0 43.6 1.0 N C:CYS119 5.0 46.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl504 b:62.3 occ:1.00 CLAW D:CHW504 0.0 62.3 1.0 CAV D:CHW504 1.8 56.4 1.0 CAP D:CHW504 2.7 56.0 1.0 CAU D:CHW504 2.7 52.9 1.0 OAQ D:CHW504 2.9 52.8 1.0 CAX D:CHW504 3.0 51.8 1.0 CG2 D:THR219 3.3 37.3 1.0 SG D:CYS119 3.6 41.8 1.0 CB D:THR219 3.9 36.3 1.0 NE D:ARG118 3.9 45.5 1.0 CAC D:CHW504 4.0 55.7 1.0 CAO D:CHW504 4.1 53.5 1.0 CD D:ARG118 4.1 43.9 1.0 CD1 D:LEU122 4.3 33.1 1.0 OG1 D:THR219 4.4 37.1 1.0 CZ D:TYR220 4.4 39.4 1.0 CAB D:CHW504 4.6 52.6 1.0 OH D:TYR220 4.6 36.8 1.0 CE1 D:TYR220 4.6 38.8 1.0 CE2 D:TYR220 4.6 41.6 1.0 CA D:CYS119 4.7 44.5 1.0 CG D:ARG118 4.8 42.7 1.0 CB D:CYS119 4.8 44.3 1.0 O D:ALA216 4.9 38.4 1.0

T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita. Insights Into the Ubiquinol/Dioxygen Binding and Proton Relay Pathways of the Alternative Oxidase. Biochim Biophys Acta V.1860 375 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 30910528
DOI: 10.1016/J.BBABIO.2019.03.008